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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattgagtttcctcatttgttttctcgtcctaattccttttttatttcccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATCACGAAAAAAAAAACGTATACTTGGCAAACGCGATGGTGGATTCTGAATT

Basic information

species Selaginella moellendorffii
transcript EFJ09546
intron # 13
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169045510|gb|FE450703.1|FE450703
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|70669704|gb|DN838281.1|DN838281
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169041728|gb|FE449299.1|FE449299
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169115409|gb|FE516150.1|FE516150
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169060191|gb|FE467553.1|FE467553
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169054032|gb|FE461331.1|FE461331
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCATTCGATTTTTGTGAATGAG                         GACCAGCTAGAGAACCAAGCATGAATATTGTTGAGAAACTTATAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169106154|gb|FE507946.1|FE507946
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169052818|gb|FE461196.1|FE461196
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169099587|gb|FE502620.1|FE502620
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169029568|gb|FE438929.1|FE438929
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169096935|gb|FE497065.1|FE497065
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169078720|gb|FE487555.1|FE487555
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCATTCGATTTTTGTGAATGAG                         GACCAGCTAGAGAACCAAGCATGAATATTGTTGAGAAACTTATAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169078771|gb|FE489621.1|FE489621
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCATTCGATTTTTGTGAATGAG                         GACCAGCTAGAGAACCAAGCATGAATATTGTTGAGAAACTTATAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169088168|gb|FE493394.1|FE493394
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169075080|gb|FE481453.1|FE481453
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCATTCGATTTTTGTGAATGAG                         GACCAGCTAGAGAACCAAGCATGAATATTGTTGAGAAACTTATAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
EST: gi|169088396|gb|FE495442.1|FE495442
EST:     CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAG                         GATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC
genomic: CGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 34 (downstream exon)
Score: 47

AGTCGTGATTGATGCCAAGACAATGGCAGCCGATCCAGTTGCTGTGGTCTCGATCCCTGTAAGGATTCCTTATGGTTTCCACTCGATTTTTGTGAATGAGgtgagattga ... ccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATCACGAAAAAAAAAACGTATACTTGGCAAACGCGATGGTGGATTCTGAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtttcctcatttgttttctcgtcctaattccttttttatttcccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATCACGAAAAAAAAAACGTATACTTGGCAAACGCGATGGTGGATTCTGAATT
                        tcctaat  putative branch site (score: 47)
            tttgttttctcgtcct  CT-rich tract
                           taattccttttttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattgagtttcctcatttgttttctcgtcctaattccttttttatttcccgagtttagGATCAGCTAGGGAACCAAGCATGAATATTGTTGAGAAACTTACAATTGATCACGAAAAAAAAAACGTATACTTGGCAAACGCGATGGTGGATTCTGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA